Alignments for a candidate for lysA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Pseudomonas putida KT2440

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate PP_5227 PP_5227 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__Putida:PP_5227
          Length = 415

 Score =  540 bits (1392), Expect = e-158
 Identities = 269/417 (64%), Positives = 333/417 (79%), Gaps = 2/417 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M+ FNY+ DG+L+AE V L+ +A +YGTP YVYSRA +E  + ++  ++    HL+C+AV
Sbjct: 1   MNAFNYR-DGELFAEGVALSAIAERYGTPTYVYSRAHIEAQYRSYADALQGTEHLVCFAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNLGVLN LARLG+GFDIVS GELERVLAAGG   +VVFSGVGKT  +M+RAL++ +
Sbjct: 60  KANSNLGVLNVLARLGAGFDIVSGGELERVLAAGGRADRVVFSGVGKTREDMRRALEVGV 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVES  EL+RL  VA E+G  AP+SLR+NPDVDA THPYISTGL++NKFGI    A 
Sbjct: 120 HCFNVESTDELERLQVVAAEMGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAIADAE 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            +Y  A  LPNL+V G+DCHIGSQLT + PF+DA DRLL L+D L   GIH+RHLD+GGG
Sbjct: 180 AIYVRAAQLPNLEVVGVDCHIGSQLTTVEPFLDALDRLLVLVDRLAECGIHLRHLDLGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           +GV YRDE PP+ ++Y KA+ +R+   RDL L+FEPGR I ANAGVL+T+VE+LKHTEHK
Sbjct: 240 VGVRYRDEQPPRVADYIKAIRERV-GERDLALVFEPGRYIVANAGVLLTRVEYLKHTEHK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360
           +FAIIDAAMNDLIRPALYQAW  +  ++PR GE + YDLVGP+CET DFLGKDR L L E
Sbjct: 299 DFAIIDAAMNDLIRPALYQAWMGVSAVKPRAGEGRAYDLVGPICETGDFLGKDRVLNLAE 358

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417
           GDLLAV S+GAYGF MSSNYNTR R AE++VDG++ + VR+RE ++ L+A ES+LPE
Sbjct: 359 GDLLAVESAGAYGFVMSSNYNTRGRCAEILVDGDQAFEVRRRETVAELYAGESLLPE 415


Lambda     K      H
   0.319    0.137    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 544
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate PP_5227 PP_5227 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01048.hmm
# target sequence database:        /tmp/gapView.1394.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-163  527.8   0.0   8.7e-163  527.6   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5227  PP_5227 diaminopimelate decarbox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5227  PP_5227 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.6   0.0  8.7e-163  8.7e-163       4     416 ..       6     410 ..       3     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 527.6 bits;  conditional E-value: 8.7e-163
                           TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldv 78 
                                          +dgel++egv+l ++ae++gtP+Yvy+++++++++++++ a +++e+lv++AvKAnsnl vl++la++G+g+d+
  lcl|FitnessBrowser__Putida:PP_5227   6 YRDGELFAEGVALSAIAERYGTPTYVYSRAHIEAQYRSYADALQGTEHLVCFAVKANSNLGVLNVLARLGAGFDI 80 
                                         5799*********************************************************************** PP

                           TIGR01048  79 vsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvd 153
                                         vsgGEler+laAg +a+++vfsg+gk++e++++ale++++++nv+s++ele+l+ +a+e+gk a+v+lRvnpdvd
  lcl|FitnessBrowser__Putida:PP_5227  81 VSGGELERVLAAGGRADRVVFSGVGKTREDMRRALEVGVHCFNVESTDELERLQVVAAEMGKVAPVSLRVNPDVD 155
                                         *************************************************************************** PP

                           TIGR01048 154 aktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegie 228
                                         a th+yisTGlke+KFGi++++ae++y +a++l++le+vG+++HIGSq++ +epf +a+++++ l+++l+e gi+
  lcl|FitnessBrowser__Putida:PP_5227 156 AGTHPYISTGLKENKFGIAIADAEAIYVRAAQLPNLEVVGVDCHIGSQLTTVEPFLDALDRLLVLVDRLAECGIH 230
                                         *************************************************************************** PP

                           TIGR01048 229 leeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrk 303
                                         l++ldlGGG+g++y++e+ +p++++y +++ e++ +     ++l l++EpGR++vanagvlltrVe++K++e++ 
  lcl|FitnessBrowser__Putida:PP_5227 231 LRHLDLGGGVGVRYRDEQ-PPRVADYIKAIRERVGE-----RDLALVFEPGRYIVANAGVLLTRVEYLKHTEHKD 299
                                         ****************99.************99999.....6********************************* PP

                           TIGR01048 304 fvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYga 378
                                         f+++Da+mndliRpalY+a++ ++a+ + ++ e   +d+vGp+CE+gD+l+kdr l+ +e Gdllav+saGAYg+
  lcl|FitnessBrowser__Putida:PP_5227 300 FAIIDAAMNDLIRPALYQAWMGVSAV-KPRAGEGRAYDLVGPICETGDFLGKDRVLNLAE-GDLLAVESAGAYGF 372
                                         **************************.6788999**********************9999.************** PP

                           TIGR01048 379 smssnYnsrprpaevlveegkarlirrretledllale 416
                                          mssnYn+r+r+ae+lv++++a  +rrret+++l a e
  lcl|FitnessBrowser__Putida:PP_5227 373 VMSSNYNTRGRCAEILVDGDQAFEVRRRETVAELYAGE 410
                                         *********************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (415 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.50
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis